Publications

Authors:

Campagna, Davide; Gasparini, Fabio; Franchi, Nicola; Manni, Lucia; Telatin, Andrea; Vitulo, Nicola; Ballarin, Loriano; Valle, Giorgio

Title:

SATRAP: SOLiD Assembler TRAnslation Program

Year:

2015

Type of item:

Articolo in Rivista

Tipologia ANVUR:

Articolo su rivista

Language:

Inglese

Referee:

No

Name of journal:

PLoS ONE

ISSN of journal:

1932-6203

N° Volume:

10

Number or Folder:

9

Page numbers:

275-291

Keyword:

Algorithms; High-Throughput Nucleotide Sequencing; Sequence Analysis, RNA; Computer Simulation; Software; Transcriptome

Short description of contents:

SOLiD DNA sequences are typically analyzed using a reference genome, while they are not recommended for de novo assembly of genomes or transcriptomes. This is mainly due to the difficulty in translating the SOLiD color-space data into normal base-space sequences. In fact, the nature of color-space is such that any misinterpreted color leads to a chain of further translation errors, producing totally wrong results. Here we describe SATRAP, a computer program designed to efficiently translate de novo assembled color-space sequences into a base-space format. The program was tested and validated using simulated and real transcriptomic data; its modularity allows an easy integration into more complex pipelines, such as Oases for RNA-seq de novo assembly. SATRAP is available at http://satrap.cribi.unipd.it, either as a multi-step pipeline incorporating several tools for RNA-seq assembly or as an individual module for use with the Oases package.

Product ID:

93999

Handle IRIS:

11562/951758

Last Modified:

November 26, 2022

Bibliographic citation:

Campagna, Davide; Gasparini, Fabio; Franchi, Nicola; Manni, Lucia; Telatin, Andrea; Vitulo, Nicola; Ballarin, Loriano; Valle, Giorgio, SATRAP: SOLiD Assembler TRAnslation Program «PLoS ONE» , vol. 10 , n. 9 , 2015 , pp. 275-291

Consulta la scheda completa presente nel repository istituzionale della Ricerca di Ateneo